求助：acpype运行错误

kay · 发表于 Post on 2019-12-20 15:52:58

本帖最后由 kay 于 2019-12-21 10:13 编辑

刚刚学习gromacs，acpype运行错误解决不了./acpype.py -i bcz.mol2
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2019 AWSdS |
============================================================================
WARNING: no 'babel' executable, no PDB file as input can be used!
==> ... charge set to 0
==> Executing Antechamber...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

For atom[33]:B33, the best APS is not zero, bonds involved by this atom are frozen

Info: Bond types are assigned for valence state 1 with penalty of 1
Running: /home/software/amber14-Intel/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

Running: /home/software/amber14-Intel/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 264; net charge: 0

Running: /home/software/amber14-Intel/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/home/software/amber14-Intel/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Antechamber failed
==> * Parmchk OK *
ERROR: Tleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'bcz_AC.inpcrd'
Total time of execution: less than a second

这里问题是什么呢，Ar我换成了ar，尝试了其他的体系，包括阴离子，并没有报错，不清楚这个错误是什么，还请老师给看下怎么解决。

liyuanhe211 · 发表于 Post on 2019-12-20 16:53:22

缺硼的参数

kay · 发表于 Post on 2019-12-20 17:01:30

liyuanhe211 发表于 2019-12-20 16:53
缺硼的参数

问下老师，在哪里哪里缺了硼的参数呢，具体缺了什么参数，应该怎么样添加呢，不太清楚怎么弄，还请老师指点一下。

sobereva · 发表于 Post on 2019-12-20 17:21:44

GAFF本来就不支持硼，看原文和GAFF.dat里的原子类型定义便知

kay · 发表于 Post on 2019-12-20 18:34:30

sobereva 发表于 2019-12-20 17:21
GAFF本来就不支持硼，看原文和GAFF.dat里的原子类型定义便知

好的，老师，我去看了一下，确实没有定义，那对于这个体系我该怎样做呢？

liyuanhe211 · 发表于 Post on 2019-12-20 19:17:13

kay 发表于 2019-12-20 18:34
好的，老师，我去看了一下，确实没有定义，那对于这个体系我该怎样做呢？

补它的参数呗，取决于目的，查文献、自己做拟合、抄类似原子参数等等。

kay · 发表于 Post on 2019-12-20 21:19:56

liyuanhe211 发表于 2019-12-20 19:17
补它的参数呗，取决于目的，查文献、自己做拟合、抄类似原子参数等等。

我还有两点疑问，请教一下老师，1是我这个错误应该是在用sqm做电荷计算的时候出的问题吧，那我解决这个问题的方法是不是需要在脚本里面把这一步注释掉，然后自己用gaussian算一下这个体系的电荷。2是Antechamber不是会自动对分子指认GAFF或者AMBER立场参数，没参数的会自动通过半经验方法来计算么，这里不是会自动计算适合用于分子模拟目的的AM1-BCC电荷么？为什么在这里没有自动去计算呢

sobereva · 发表于 Post on 2019-12-21 01:44:25

1 暂且不提硼的事，凡是碰到sqm模块半经验计算卡住，首先用-c user跳过产生原子电荷计算步骤，然后用Multiwfn产生RESP电荷自己补进去，明显比AM1-BCC更适合动力学计算，看
RESP拟合静电势电荷的原理以及在Multiwfn中的计算
http://sobereva.com/441（http://bbs.keinsci.com/thread-10880-1-1.html）
Multiwfn对于含有任意元素的体系都可以算RESP电荷，不像antechamber碰到GAFF不支持的元素连电荷都算不了

2 算原子电荷和补成键参数是两码事。就算你不让antechamber计算电荷，对于遇到硼这种GAFF不支持的元素，antechamber也没法搞。

由于硼的情况很复杂，所以主流力场都不支持硼。一般都需要自己根据实际体系来拟合力场参数。

kay · 发表于 Post on 2019-12-21 10:12:54

sobereva 发表于 2019-12-21 01:44
1 暂且不提硼的事，凡是碰到sqm模块半经验计算卡住，首先用-c user跳过产生原子电荷计算步骤，然后用Multiw ...

明白，谢谢老师

naoki · 发表于 Post on 2019-12-21 13:06:35

可以用OPLS力场试试

wgg1181543722 · 发表于 Post on 2019-12-21 23:30:24

像力场里不存在的，你可以在mol2文件里把它替换成已知的，像图片里这种，产生力场文件后，修改一些参数就可以

kay · 发表于 Post on 2019-12-23 09:51:14

sobereva 发表于 2019-12-21 01:44
1 暂且不提硼的事，凡是碰到sqm模块半经验计算卡住，首先用-c user跳过产生原子电荷计算步骤，然后用Multiw ...

老师，我用-c user命令并没有起到效果，不知道这个错误的原因（是缺少B和其他原子的成键信息么），这里该怎样做呢？麻烦老师指点一下============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2019 AWSdS |
============================================================================
WARNING: no 'babel' executable, no PDB file as input can be used!
==> Reading user's charges from mol2 file...
==> ... charge set to 0
==> Executing Antechamber...
==> AC output file present... doing nothing
==> * Antechamber OK *
==> * Parmchk OK *
==> Executing Tleap...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Checking 'MOL'....
Checking parameters for unit 'MOL'.
Checking for bond parameters.
Could not find bond parameter for: os - B
Could not find bond parameter for: B - os
Could not find bond parameter for: B - f
Could not find bond parameter for: B - f
Checking for angle parameters.
Could not find angle parameter: cd - ce - os
Could not find angle parameter: ce - os - B
Could not find angle parameter: ce - ce - os
Could not find angle parameter: ce - cf - os
Could not find angle parameter: os - B - os
Could not find angle parameter: os - B - f
Could not find angle parameter: os - B - f
Could not find angle parameter: cf - os - B
Could not find angle parameter: os - B - f
Could not find angle parameter: os - B - f
Could not find angle parameter: f - B - f
There are missing parameters.
Unit is OK.
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-I: Adding /home/software/amber14-Intel/dat/leap/prep to search path.
-I: Adding /home/software/amber14-Intel/dat/leap/lib to search path.
-I: Adding /home/software/amber14-Intel/dat/leap/parm to search path.
-I: Adding /home/software/amber14-Intel/dat/leap/cmd to search path.
-f: Source tleap.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap.in
Could not open file leaprc.protein.ff14SB: not found
----- Source: /home/software/amber14-Intel/dat/leap/cmd/leaprc.gaff
----- Source of /home/software/amber14-Intel/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/software/amber14-Intel/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.7, Nov 2013)
Loading parameters: ./bcz_AC.frcmod
Reading title:
Loading Mol2 file: ./bcz_user_gaff.mol2
Reading MOLECULE named Molecule
Checking 'MOL'....
Checking parameters for unit 'MOL'.
Checking for bond parameters.
Could not find bond parameter for: os - B
Could not find bond parameter for: B - os
Could not find bond parameter for: B - f
Could not find bond parameter for: B - f
Checking for angle parameters.
Could not find angle parameter: cd - ce - os
Could not find angle parameter: ce - os - B
Could not find angle parameter: ce - ce - os
Could not find angle parameter: ce - cf - os
Could not find angle parameter: os - B - os
Could not find angle parameter: os - B - f
Could not find angle parameter: os - B - f
Could not find angle parameter: cf - os - B
Could not find angle parameter: os - B - f
Could not find angle parameter: os - B - f
Could not find angle parameter: f - B - f
There are missing parameters.
Unit is OK.
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<MOL 1>.A<B33 33> Could not find vdW (or other) parameters for type: B
Parameter file was not saved.
Saving MOL.
Building topology.
Building atom parameters.
Quit
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Tleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'bcz_AC.inpcrd'
Total time of execution: less than a second

kay · 发表于 Post on 2019-12-23 09:52:22

wgg1181543722 发表于 2019-12-21 23:30
像力场里不存在的，你可以在mol2文件里把它替换成已知的，像图片里这种，产生力场文件后，修改一些参数就可 ...

谢谢，我尝试了你说的这种做法，还是报同样的错误，这种做法和sob老师说的用-c user是一个道理吧，但是我用-c user还是报错

kay · 发表于 Post on 2019-12-23 09:52:39

naoki 发表于 2019-12-21 13:06
可以用OPLS力场试试

好的，谢谢，学习一下

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